Evidence map›Paper›PMID 37165019›Full record

ArticleScientific reports2023

SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay.

Olivier Pernet, Maia Weisenhaus, Chrysovalantis Stafylis, Christopher Williams, Mihaela Campan, Jonas Pettersson, Nicole Green, David M Lee, Paul D Thomas, Pamela Ward and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.6field-weighted citation impact, top 36% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed, 3 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 2 institutions in 1 country.

Olivier PernetDepartment of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA. pernet@usc.edu.
Maia WeisenhausDepartment of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA.
Chrysovalantis StafylisDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
Christopher WilliamsDepartment of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA.
Mihaela CampanDepartment of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA.
Jonas PetterssonDepartment of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA.
Nicole GreenLos Angeles County Department of Public Health, Los Angeles, CA, USA.
David M LeeDepartment of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA.
Paul D ThomasDepartment of Preventive Medicine, Division of Bioinformatics, University of Southern California, Los Angeles, CA, USA.
Pamela WardDepartment of Pathology & Laboratory Medicine in Keck, University of Southern California, Los Angeles, CA, USA.
Howard HuDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
Jeffrey D KlausnerDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA.
Andrea A Z KovacsDepartment of Pediatrics, Maternal, Child and Adolescent Center for Infectious Diseases and Virology, University of Southern California, Los Angeles, CA, USA.
U. S. C. Variant Study Group
University of Southern California · USLos Angeles County Department of Public Health · US

Funding

Long-term Effects of IDU, HIV, HCV and the Impact of HCV Cure on Immune Activation and Liver Fibrosis in Aging WomenR01DA044111 · NIDA · UNIVERSITY OF SOUTHERN CALIFORNIA · PI KOVACS, ANDREA A.Z., TIEN, PHYLLIS C · 2017 to 2021
$3.5M
NIDA NIH HHS R01 DA044111
6 · The paper itself

Abstract

Epidemiologic surveillance of circulating SARS-CoV-2 variants is essential to assess impact on clinical outcomes and vaccine efficacy. Whole genome sequencing (WGS), the gold-standard to identify variants, requires significant infrastructure and expertise. We developed a digital droplet polymerase chain reaction (ddPCR) assay that can rapidly identify circulating variants of concern/interest (VOC/VOI) using variant-specific mutation combinations in the Spike gene. To validate the assay, 800 saliva samples known to be SARS-CoV-2 positive by RT-PCR were used. During the study (July 2020-March 2022) the assay was easily adaptable to identify not only existing circulating VAC/VOI, but all new variants as they evolved. The assay can discriminate nine variants (Alpha, Beta, Gamma, Delta, Eta, Epsilon, Lambda, Mu, and Omicron) and sub-lineages (Delta 417N, Omicron BA.1, BA.2). Sequence analyses confirmed variant type for 124/124 samples tested. This ddPCR assay is an inexpensive, sensitive, high-throughput assay that can easily be adapted as new variants are identified.

Indexed as

COVID-19SARS-CoV-2Clinical Decision-MakingCOVID-19 TestingHumansPolymerase Chain ReactionPopulation Surveillance

Identifiers

PMID37165019
PMCPMC10170421
OpenAlexW4376133528

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.